Impairment of the photosynthetic apparatus by oxidative stress induced by photosensitization reaction of protoporphyrin IX

Treatment with the herbicide acifluorfen-sodium (AF-Na), an inhibitor of protoporphyrinogen oxidase, caused an accumulation of protoporphyrin IX (Proto IX) , light-induced necrotic spots on the cucumber cotyledon within 12-24 h, and photobleaching after 48-72 h of light exposure. Proto IX-sensitized and singlet oxygen (¹O₂)-mediated oxidative stress caused by AF-Na treatment impaired photosystem I (PSI), photosystem II (PSII) and whole chain electron transport reactions. As compared to controls, the F_v/F_m (variable to maximal chlorophyll a fluorescence) ratio of treated samples was reduced. The PSII electron donor NH₂OH failed to restore the F_v/F_m ratio suggesting that the reduction of F_v/F_m reflects the loss of reaction center functions. This explanation is further supported by the practically near-similar loss of PSI and PSII activities. As revealed from the light saturation curve (rate of oxygen evolution as a function of light intensity), the reduction of PSII activity was both due to the reduction in the quantum yield at limiting light intensities and impairment of light-saturated electron transport. In treated cotyledons both the Q (due to recombination of Q_A⁻ with S₂) and B (due to recombination of Q_B⁻ with S₂/S₃) band of thermoluminescence decreased by 50% suggesting a loss of active PSII reaction centers. In both the control and treated samples, the thermoluminescence yield of B band exhibited a periodicity of 4 suggesting normal functioning of the S states in centers that were still active. The low temperature (77 K) fluorescence emission spectra revealed that the F₆₉₅ band (that originates in CP-47) increased probably due to reduced energy transfer from the CP47 to the reaction center. These demonstrated an overall damage to the PSI and PSII reaction centers by ¹O₂ produced in response to photosensitization reaction of protoporphyrin IX in AF-Na-treated cucumber seedlings.     

Comparison of five rep-PCR genomic fingerprinting methods for differentiation of fecal Escherichia coli from humans, poultry and wild birds

The development of a methodology to identify the origin of fecal pollution is important both for assessing the degree of risk posed to public health and for developing strategies to mitigate the environmental loading of pathogens associated with waterborne disease transmission. Five rep-PCR genomic fingerprinting methods, such as rep-PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR, ERIC2-PCR, BOX-PCR and (GTG)(5)-PCR, were assessed for their potential in differentiation of 232 fecal Escherichia coli isolates obtained from humans, poultry (chicken, duck and turkey) and wild birds (Canada goose and gull). Based on the results of cluster analysis and discriminant function analysis, (GTG)(5)-PCR was found to be the most suitable method for molecular typing of fecal E. coli, followed by BOX-PCR, REP-PCR, ERIC-PCR and ERIC2-PCR. A discriminant function analysis of (GTG)(5)-PCR fingerprints showed that 94.1%, 79.8%, 80.5%, 74.4%, 86.7% and 88.6% of turkey, chicken, duck, Canada goose, gull and human E. coli isolates were classified into the correct host group, respectively. Subsequently, (GTG)(5)-PCR was tested for its ability to track the origin of 113 environmental E. coli isolated from natural pond water. In conclusion, the (GTG)(5)-PCR genomic fingerprinting method can be considered as a promising genotypic tool for epidemiological surveillance of fecal pollution in aquatic environments.     

Evaluation of repetitive extragenic palindromic-PCR for discrimination of fecal Escherichia coli from humans, and different domestic- and wild-animals

The objective of this study was to investigate the potential of repetitive extragenic palindromic anchored polymerase chain reaction (rep-PCR) in differentiating fecal Escherichia coli isolates of human, domestic- and wild-animal origin that might be used as a molecular tool to identify the possible source(s) of fecal pollution of source water. A total of 625 fecal E. coli isolates of human, 3 domestic- (cow, dog and horse) and 7 wild-animal (black bear, coyote, elk, marmot, mule deer, raccoon and wolf) species were characterized by rep-PCR DNA fingerprinting technique coupled with BOX A1R primer and discriminant analysis. Discriminant analysis of rep-PCR DNA fingerprints of fecal E. coli isolates from 11 host sources revealed an average rate of correct classification of 79.89%, and 84.6%, 83.8%, 83.3%, 82.5%, 81.6%, 80.8%, 79.8%, 79.3%, 77.4%, 73.2% and 63.6% of elk, human, marmot, mule deer, cow, coyote, raccoon, horse, dog, wolf and black bear fecal E. coli isolates were assigned to the correct host source. These results suggest that rep-PCR DNA fingerprinting procedures can be used as a source tracking tool for detection of human- as well as animal-derived fecal contamination of water.     

A Combined Gene Signature of Hypoxia and Notch Pathway in Human Glioblastoma and Its Prognostic Relevance

Hypoxia is a hallmark of solid tumors including glioblastoma (GBM). Its synergism with Notch signaling promotes progression in different cancers. However, Notch signaling exhibits pleiotropic roles and the existing literature lacks a comprehensive understanding of its perturbations under hypoxia in GBM with respect to all components of the pathway. We identified the key molecular cluster(s) characteristic of the Notch pathway response in hypoxic GBM tumors and gliomaspheres. Expression of Notch and hypoxia genes was evaluated in primary human GBM tissues by q-PCR. Clustering and statistical analyses were applied to identify the combination of hypoxia markers correlated with upregulated Notch pathway components. We found well-segregated tumor—clusters representing high and low HIF-1α/PGK1-expressors which accounted for differential expression of Notch signaling genes. In combination, a five-hypoxia marker set (HIF-1α/PGK1/VEGF/CA9/OPN) was determined as the best predictor for induction of Notch1/Dll1/Hes1/Hes6/Hey1/Hey2. Similar Notch-axis genes were activated in gliomaspheres, but not monolayer cultures, under moderate/severe hypoxia (2%/0.2% O₂). Preliminary evidence suggested inverse correlation between patient survival and increased expression of constituents of the hypoxia-Notch gene signature. Together, our findings delineated the Notch-axis maximally associated with hypoxia in resected GBM, which might be prognostically relevant. Its upregulation in hypoxia-exposed gliomaspheres signify them as a better in-vitro model for studying hypoxia-Notch interactions than monolayer cultures.     

Fisheries enhancement and biodiversity assessment of fish,prawn and mud crab in Chilika lagoon through hydrological intervention

The degraded state of the fragile ecosystem of Chilika lagoon on the east coast of India caused by natural changes and anthropogenic pressure was in the process of restoration through an effective hydrological intervention during 2000 after thorough scientific investigation including EIA study. The rich fisheries of Chilika lagoon that support livelihood of 0.2 million local fisherfolk was in dwindling state during the eco-degradation phase. Studies on fisheries and fish biodiversity of the lagoon for 4 years before and 4 years after the intervention showed the stark and rapid recovery of fishery immediately after opening of the new mouth with sixfold increase in average annual landing. The average productivity (11.3 t km⁻²) and CPUE (6.2 kg boat-day⁻¹) during post intervention phase registered 528 and 464% increase, as compared to Pre-intervention years. In total, 277 species of fish and shell fish were documented as occurring in Chilika lagoon before the hydrological intervention. Inventory survey for fish and shell fish species diversity during and after hydrological intervention documented 68 and 97 species, respectively. New records of 56 species of fish and shell fish (7 freshwater, 20 brackishwater and 29 marine) were documented from Chilika lagoon after the hydrological intervention. Analysis of commercial catches showed that the migratory species contributed to the bulk of catches (75% by species and 68% by catch weight). Fish yield and biodiversity seemed to be very sensitive to salinity and hydrologic dynamics of the lagoon. Correlation analysis indicated inverse relationship between water transparency and fish catch (R ² = 0.715; d.f. = 25; P < 0.01). Positive correlation between salinity and prawn landing (R ² = 0.542; d.f. = 25; P < 0.01) and salinity and mud crab landing (R ² = 0.628; d.f. = 25; P < 0.001). Average salinity for the whole lagoon was significantly increased by 42.7% (P < 0.007) as compared to pre-intervention situation. Maintenance of estuarine character of Chilika’s ecosystem particularly the salinity gradient, un-hindered auto-recruitment of fish and shell fish and prevention of destructive fishing are the key factors for fisheries enhancement. Unless carefully planned conservation and regulation measures are ensured with the active participation of local communities during the early phase of restoration, the present scenario of fisheries enhancement may not sustain for longer time.     

Sensitive estimation of total cholesterol in blood using Au nanowires based micro-fluidic platform

Determination of cholesterol level in blood is important in clinical applications. In this work, modified Au nanowires-electrochemical biosensor based on MEMS micro-fluidic platform is proposed for estimating total cholesterol in blood. This sensor consists of "aligned" Au nanowires as working electrode, platinum counter electrode deposited on the silicon platform and Ag/AgCl (3M KCl) reference electrode. The "aligned" Au nanowires are immobilized with cholesterol oxidase and cholesterol esterase using specific covalent chemistry. Further, Au nanowires promotes better electron transfer between the enzymes and electrodes, because of their large surface to volume ratio, small diffusion time, large electrical conductivity and their aligned nature. The modified Au nanowires showed a stable calibration line and a quasi-linear relationship between cholesterol level and current response in the range of 1-6 mM (in steps of 1 mM over the baseline blood serum). The sensitivity of the modified electrode was found to be about 69 nA/mM with good storage and interference stability.     

Production of tannase by the immobilized cells of Bacillus licheniformis KBR6 in Ca-alginate beads

AIMS: The present study was aimed at finding the optimal conditions for immobilization of Bacillus licheniformis KBR6 cells in calcium-alginate (Ca-alginate) beads and determining the operational stability during the production of tannin-acyl-hydrolase (tannase) under semicontinous cultivation. METHODS AND RESULTS: The active cells of B. licheniformis KBR6 were immobilized in Ca-alginate and used for the production of tannase. The influence of alginate concentration (5, 10, 20 and 30 g l(-1)) and initial cell loading on enzyme production were studied. The production of tannase increased significantly with increasing alginate concentration and reached a maximum enzyme yield of 0.56 +/- 0.03 U ml(-1) at 20 g l(-1). This was about 1.70-fold higher than that obtained by free cells. The immobilized cells produced tannase consistently over 13 repeated cycles and reached a maximum level at the third cycle. Scanning electron microscope study indicated that the cells in Ca-alginate beads remain in normal shape. CONCLUSIONS: The Ca-alginate entrapment is a promising immobilization method of B. licheniformis KBR6 for repeated tannase production. Tannase production by immobilized cells is superior to that of free cells because it leads to higher volumetric activities within the same period of fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report of tannase production from immobilized bacterial cells. The bacterium under study can produce higher amounts of tannase with respect to other fungal strains within a short cultivation period.     

Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes

The high-quality rice genome sequence is serving as a reference for comparative genome analysis in crop plants, especially cereals. However, early comparisons with bread wheat showed complex patterns of conserved synteny (gene content) and colinearity (gene order). Here, we show the presence of ancient duplicated segments in the progenitor of wheat, which were first identified in the rice genome. We also show that single-copy (SC) rice genes, those representing unique matches with wheat expressed sequence tag (EST) unigene contigs in the whole rice genome, show more than twice the proportion of genes mapping to syntenic wheat chromosome as compared to the multicopy (MC) or duplicated rice genes. While 58.7% of the 1,244 mapped SC rice genes were located in single syntenic wheat chromosome groups, the remaining 41.3% were distributed randomly to the other six non-syntenic wheat groups. This could only be explained by a background dispersal of genes in the genome through transposition or other unknown mechanism. The breakdown of rice–wheat synteny due to such transpositions was much greater near the wheat centromeres. Furthermore, the SC rice genes revealed a conserved primordial gene order that gives clues to the origin of rice and wheat chromosomes from a common ancestor through polyploidy, aneuploidy, centromeric fusions, and translocations. Apart from the bin-mapped wheat EST contigs, we also compared 56,298 predicted rice genes with 39,813 wheat EST contigs assembled from 409,765 EST sequences and identified 7,241 SC rice gene homologs of wheat. Based on the conserved colinearity of 1,063 mapped SC rice genes across the bins of individual wheat chromosomes, we predicted the wheat bin location of 6,178 unmapped SC rice gene homologs and validated the location of 213 of these in the telomeric bins of 21 wheat chromosomes with 35.4% initial success. This opens up the possibility of directed mapping of a large number of conserved SC rice gene homologs in wheat. Overall, only 46.4% of these SC genes code for proteins with known functional domains; the remaining 53.6% have unknown function, and hence, represent an important, but yet, under explored category of genes. Electronic supplementary material Supplementary material is available for this article at and is accessible for authorized users.     

Effects of Nutrients at Different Salinities on Growth of the Freshwater Green Alga Scenedesmus bijugatus in Water of Narendra Pond,Puri, Orissa

The growth and biochemical composition of Scenedesmus bijugatus grown in normal and nutrient enriched Narendra Pond water was evaluated at different levels of salinity. In normal pond water (NPW) the growth was enhanced when the initial salinity of the water was doubled (to 7.2 mmol/l) but further salinity increase caused growth retardation. In nutrient enriched pond water (NEW), however, the maximum growth occurred in the culture containing 29 mmol/l of NaCl. At growth retarding salt concentrations the chlorophyll, carbohydrate, protein and lipid contents per cell decreased in both NPW and NEW while the proline content first increased and was then reduced. All nutrients, taken separately or in combination, caused growth enhancement of the alga at the three selected salinity levels. The alga showed a better halotolerance when enriched with nitrogen or phosphorus.     

Isolating plant genomic DNA without liquid nitrogen

DNA was isolated from leaves of 10 plant species (Cuminum cyminum, Vigna aconitifolia, Pennisetum typhoides, Tecoma stans, Lycium barbarum, Anogeissus acuminata, Tecomella undulata, Zizyphus mauritiana, Phoenix dactylifera, andEruca sativa) and a fungus (Fusarium oxysporum) using the CTAB method. Three fixing solutions (alcohol, alcohol and chloroform, alcohol and EDTA) were used to produce high molecular weight DNA (>40 kb). DNA quality and quantity was comparable for the 3 fixing solutions and liquid nitrogen grinding. Adding chloroform or EDTA to fixing solutions offered no advantage over absolute alcohol. Isolated DNA was suitable for RAPD analysis, restriction digestion, and cloning. This method does not require liquid nitrogen for fixation, grinding, or storage at −80°C, making it advantagenous over other common protocols.